Contacts of the strand formed by residues 635 - 640 (chain A) in PDB entry 3EA4
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 635 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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558A VAL 3.1 7.8 + - - +
559A LYS* 3.5 5.5 - - + +
560A VAL* 2.8 34.2 + - - +
610A ILE* 3.9 4.2 - - - +
611A PRO* 3.5 24.9 - - + -
612A ALA* 4.2 3.4 - - - -
613A ALA* 3.4 29.5 + - + +
624A ALA 5.0 1.1 + - - -
627A THR* 3.7 21.9 - - + +
628A MET* 3.6 41.4 - - + +
631A THR* 3.6 37.7 - - + +
633A GLY 3.9 1.3 + - - +
634A PRO* 1.3 74.2 - - - +
636A LEU* 1.3 87.1 + - - +
637A LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A PHE* 4.4 13.9 - - + -
548A LEU* 5.9 2.9 - - + -
560A VAL* 3.6 33.0 - - + +
562A LEU* 4.0 21.8 - - + -
601A MET* 3.3 40.8 - - + +
602A LEU* 4.2 4.0 - - + +
605A ALA* 3.8 17.5 - - + -
610A ILE* 4.1 3.7 - - + +
611A PRO 3.1 7.7 + - - -
612A ALA* 3.1 33.4 - - + -
613A ALA 3.1 6.2 + - - +
635A TYR* 1.3 77.9 - - - +
637A LEU* 1.3 65.7 + - - +
638A ASP* 4.5 1.8 - - + +
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560A VAL 2.9 9.4 + - - +
561A LEU* 3.9 12.2 - - + -
562A LEU* 3.0 27.9 + - - +
613A ALA* 3.5 25.1 - - + +
614A ARG 4.6 0.2 - - - +
615A VAL* 3.9 15.9 - - + -
624A ALA* 3.8 25.8 - - + +
625A ILE* 3.6 42.8 - - + +
628A MET* 3.9 18.4 - - - -
635A TYR* 4.0 6.8 - - + +
636A LEU* 1.3 75.4 - - - +
638A ASP* 1.3 60.4 + - - +
639A VAL* 3.4 12.3 + - + +
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Residues in contact with ASP 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562A LEU* 3.5 17.3 - - + +
564A ASN* 3.0 38.5 + - - +
597A ILE* 4.3 0.2 - - - +
601A MET* 4.5 8.6 - - + +
602A LEU* 3.9 14.8 - - + +
613A ALA 2.9 15.7 + - - +
614A ARG* 3.0 38.1 + - - +
615A VAL* 2.9 28.7 + - - +
636A LEU* 4.0 3.0 - - + +
637A LEU* 1.3 69.8 - - - +
639A VAL* 1.3 59.0 + - - +
640A ILE* 3.7 3.6 + - - +
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Residues in contact with VAL 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ILE* 3.7 36.6 - - + -
467A ALA* 4.5 1.8 - - + -
561A LEU* 4.0 27.1 - - + -
562A LEU 2.7 17.9 + - - +
563A LEU* 3.7 12.7 - - + -
564A ASN* 2.7 31.8 + - - -
615A VAL* 3.7 18.4 - - + -
621A LEU* 4.3 7.4 - - + -
637A LEU* 4.0 10.5 - - + +
638A ASP* 1.3 72.0 + - - +
640A ILE* 1.3 60.6 + - - +
641A CYS* 3.6 10.3 + - - -
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Residues in contact with ILE 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ILE* 3.5 27.9 + - - +
564A ASN* 3.6 11.7 - - + +
566A GLN* 6.2 0.2 - - + -
597A ILE* 3.9 39.9 - - + -
614A ARG* 3.7 32.3 - - + -
615A VAL 3.1 17.2 + - - +
616A THR* 4.2 23.4 - - + +
638A ASP* 3.7 15.5 - - - +
639A VAL* 1.3 71.8 - - - +
641A CYS* 1.3 66.0 + - - +
642A PRO* 4.7 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il